The immuno response of T cells requires an antigen to be recognized. We have demonstrated before with the model protein antigen Hen Egg Lysozyme (HEL), that this response to proteins involves unfolding and degradation to peptides that are recognized on the surface of antigen-presenting cells (APC) in association with the major histocompatibility complex (MHC) molecules. Previous results showed that T-cells, after activation by I-Ak type APC, respond to a synthetic 10-mer residue, HEL 51-62. Similarly, T cells after activation by I-Ek type APC, respond to a 13-mer, HEL 84-96. HPLC chromatography of the mixture extracted from MHC class II complexes of APC after treatment with HEL gave the immuno active fractions that were analyzed by MALDI-TOF and cf-FAB MS. The major components were HEL 48-63, 48-62, 48-61 for I-Ak type APC and HEL 84-97, 84-98, 84-102 for I-Ek type APC. To extend the understanding of the protein antigen processing mechanism producing the peptides that are presented to the T cells, we are working on characterizing peptides produced from a series of mutated HEL proteins. We are developing methods involving MALDI, and electrospray and nano-electrospray tandem MS to solve these important immunology problems.